The transport pathways and exchange characteristics of the Kamil Abdus Lagoon in Istanbul, Turkey, are simulated using a finite element model with a Lagrangian particle tracking module. The lagoon is in the process of being reconfigured. The simulations are performed using a draft configuration. The effect of winds and the number of particles on the e-folding time is simulated. Results show that the lagoon is strongly dominated by winds with a correlation coefficient of 0.897 between the wind and residual current magnitudes. The lagoon e-folds in 9.1 days under realistic winds and in 14.3 days when there is no wind with confidence levels of 5%. The Lagrangian study uses six simulations with particle numbers ranging between 65073 and 2730486. A methodology based on confidence levels is proposed. It is observed that approximately 784 000 particles are necessary to obtain 5% level of confidence. With a problematic history and new planning options, the lagoon has a potential to be used as an example setting, all-field study ground for anthropogenically engineered coastal ecosystems.